Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Hardware and software requirements for quantitative analysis of comparative genomic hybridization

Applied Science

Visualizing Staphylococcus aureus pathogenic membrane modification within the host infection environment by multimodal imaging mass spectrometry

Bacterial pathogens have evolved virulence factors to colonize, replicate, and disseminate within the vertebrate host. Although there is an expanding body of literature describing how bacterial pathogens regulate their virulence repertoire in response to environmental signals, it is challenging to directly visualize virulence response within the host tissue microenvironment. Multimodal imaging approaches enable visualization of host-pathogen molecular interactions. Here we demonstrate multimodal integration of high spatial resolution imaging mass spectrometry and microscopy to visualize Staphylococcus aureus envelope modifications within infected murine and human tissues. Data-driven image fusion of fluorescent bacterial reporters and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance imaging mass spectrometry uncovered S. aureus lysyl-phosphatidylglycerol lipids, localizing to select bacterial communities within infected tissue. Absence of lysyl-phosphatidylglycerols is associated with decreased pathogenicity during vertebrate colonization as these lipids provide protection against the innate immune system. The presence of distinct staphylococcal lysyl-phosphatidylglycerol distributions within murine and human infections suggests a heterogeneous, spatially oriented microbial response to host defenses.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Team Raf Van de Pla

Fermi functions for allowed beta transitions /

At head of title: Physics Division and Math Panel."Date Issued: March 7, 1952."Bibliographical references: p. 6.Operated by Carbide and Carbon Chemicals CompanyMode of access: Internet

Aripiprazole Once-Monthly in the Acute Treatment of Schizophrenia: Findings From a 12-Week, Randomized, Double-Blind, Placebo-Controlled Study

Objective: To evaluate aripiprazole once-monthly (AOM), a long-acting injectable suspension of aripiprazole, as acute treatment in patients with schizophrenia (DSM-IV-TR). Method: Adults experiencing an acute psychotic episode were randomized to 12 weeks of double-blind treatment with AOM 400 mg or placebo (October 2012-August 2013). The primary efficacy outcome was change from baseline to endpoint (week 10) in Positive and Negative Syndrome Scale (PANSS) total score. The key secondary efficacy outcome was change from baseline in Clinical Global Impressions-Severity of Illness scale (CGI-S) score. Secondary efficacy outcomes included change from baseline in PANSS positive and negative subscale and Personal and Social Performance Scale (PSP) scores. The study took place from October 2012 through August 2013. Results: Patients (N = 340; 79% male, 66% black) were randomized to AOM (n = 168) or placebo (n = 172). Least squares (LS) mean change from baseline to endpoint (week 10) favored AOM versus placebo in PANSS total (treatment difference, -15.1 [95% CI, -19.4 to -10.8]; P \u3c .0001) and CGI-S (treatment difference, -0.8 [95% CI, -1.1 to -0.6]; P \u3c .0001) scores, as it did at all other timepoints through 12 weeks (all P = .0005). LS mean change from baseline in PANSS positive and negative subscale and PSP scores favored AOM versus placebo (P \u3c .0001). Common (\u3e10%) treatment-emergent adverse events (AOM vs placebo) were increased weight (16.8% vs 7.0%), headache (14.4% vs 16.3%), and akathisia (11.4% vs 3.5%). Conclusions: Symptoms and functioning improved with AOM 400 mg versus placebo in patients with acute schizophrenia, with acceptable safety and tolerability. These data suggest that AOM 400 mg is a viable treatment option for patients experiencing an acute schizophrenia episode. (C) Copyright 2014 Physicians Postgraduate Press, Inc

Diet and the evolution of human amylase gene copy number variation.

Abstract Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch 1-3 . This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis 4 . We found that salivary amylase gene (AMY1) copy number is correlated positively with salivary amylase protein levels, and that individuals from populations with high-starch diets have on average more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the level of AMY1 copy number differentiation is unusual. This example of positive selection on a copy number variable gene is one of the first in the human genome. Higher AMY1 copy numbers and protein levels likely improve the digestion of starchy foods, and may buffer against the fitness-reducing effects of intestinal disease. Hominin evolution is characterized by significant dietary shifts, facilitated in part by the development of stone tool technology, the control of fire, and most recently the domestication of plants and animals 5-7 . Starch, for instance, has become an increasingly prominent component of the human diet, particularly among agricultural societies 8 . It stands to reason, therefore, that studies of the evolution of amylase in humans and our close primate relatives may provide insight into our ecological history. Because the human salivary amylase gene (AMY1) shows extensive variation in copy number 9,10 , we first assess whether a functional relationship exists between AMY1 copy number and the level of amylase protein expression i

Genome-wide association study identifies five new breast cancer susceptibility loci

Breast cancer is the most common cancer in women in developed countries. To identify common breast cancer susceptibility alleles, we conducted a genome-wide association study in which 582,886 SNPs were genotyped in 3,659 cases with a family history of the disease and 4,897 controls. Promising associations were evaluated in a second stage, comprising 12,576 cases and 12,223 controls. We identified five new susceptibility loci, on chromosomes 9, 10 and 11 (P = 4.6 x 10(-7) to P = 3.2 x 10(-15)). We also identified SNPs in the 6q25.1 (rs3757318, P = 2.9 x 10(-6)), 8q24 (rs1562430, P = 5.8 x 10(-7)) and LSP1 (rs909116, P = 7.3 x 10(-7)) regions that showed more significant association with risk than those reported previously. Previously identified breast cancer susceptibility loci were also found to show larger effect sizes in this study of familial breast cancer cases than in previous population-based studies, consistent with polygenic susceptibility to the disease